Methods for reducing drug-induced liver injury

ABSTRACT

The present disclosure provides methods of treating a patient with infliximab or alternative therapies to reduce the risk of developing, and/or severity of, an adverse drug reaction such as drug-induced liver injury. The methods include identifying patients at risk for developing DILI by determining the presence or absence of one or more HLA alleles in the patients.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/663,388, filed May 8, 2018, which is incorporated herein by referencein its entireity for all purposes.

BACKGROUND

Adverse drug reactions (ADRs) can occur in patients who are treated withtherapeutic agents. In particular, drug-induced liver injury (DILI) is aserious ADR that can lead to acute liver failure. Upon diagnosis ofDILI, administration of the therapeutic drug that triggered the DILI isgenerally either reduced or discontinued, but often DILI is not detectedearly enough to avoid long-term or permanent liver damage, or evendeath.

Infliximab is a monoclonal antibody that inhibits tumor necrosis factor(TNF), a cytokine that is involved in inflammatory processes such asthose that occur in autoimmune diseases. Infliximab is approved by theUnited States Food and Drug Administration (FDA) for the treatment ofvarious autoimmune disorders including rheumatoid arthritis, Crohn'sdisease, ulcerative colitis, ankylosing spondylitis, psoriaticarthritis, and plaque psoriasis; and is under investigation as apotential therapeutic agent for various other indications, includingautoimmune disorders and diseases and conditions that are not autoimmunedisorders.

Infliximab has been linked to many instances of liver injury, but thereis no information currently available to help assess a patientpopulation's risk of developing DILI. There is a need in the art topredict, manage, and prevent the development of dangerous ADRs such asDILI in patients that have been or may otherwise be prescribedinfliximab. This disclosure addresses this and other needs.

SUMMARY OF THE INVENTION

The present disclosure provides for methods of treating a subject orpatient population suffering from an autoimmune, inflammatory, or otherdisease that may be amenable to treatment with infliximab, whilereducing the risk and/or severity of drug-induced liver injury (DILI).The present inventors found that the presence of particular HLA alleles,or sets of alleles, in a subject confers to the subject a higher risk ofthe development of DILI upon administration of infliximab. Accordingly,the methods provided herein involve identifying the at-risk subject orpatient population, and reducing the risk of development and/or reducingthe severity of DILI in the subject or patient population.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof. In another aspect, thepresent disclosure provides methods for reducing the risk ofdrug-induced liver injury (DILI) in a subject while treating the subjectfor an autoimmune disease. In some embodiments, the subject has an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof. In certainembodiments, the subject has an HLA profile comprising HLA-B*39:01. Insome embodiments, the methods comprise administering to the subject atherapeutic agent for the treatment of the autoimmune disease that isnot infliximab. In some embodiments, the therapeutic agent for thetreatment of the autoimmune disease that is not infliximab is selectedfrom the group consisting of azathioprine, mercaptopurine, adalimumab,certolizumab, methotrexate, natalizumab, vedolizumab, ustekinumab,mesalamine, budesonide, hyoscyamine, celecoxib, hydroxychloroquin,etanercept, prednisone, cyclosporine, tocilizumab, meloxicam,leflunomide, sulfasalazine, abatacept, rituximab, golimumab, acitretin,secukinumab, apremilast, sarilumab, ixekizumab, and corticotropin. Inparticular embodiments, the therapeutic agent for the treatment of theautoimmune disease that is not infliximab is selected from the groupconsisting of adalimumab, certolizumab, natalizumab, ustekinumab,vedolizumab, azathioprine, cyclosporine, methotrexate, mercaptopurin,etanercept, and rituximab.

In some embodiments, the methods provided herein comprise or are relatedto treating a subject having an autoimmune disease, wherein the subjecthas an HLA profile comprising at least one HLA allele selected from thegroup consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof. In some embodiments, the autoimmune diseaseis selected from the group consisting of Crohn's disease, ulcerativecolitis, rheumatoid arthritis, ankylosing spondylitis, psoriaticarthritis, and plaque psoriasis.

In further embodiments, the autoimmune disease is rheumatoid arthritis,ankylosing spondylitis, or psoriatic arthritis; and the therapeuticagent for the treatment of the autoimmune disease that is not infliximabis selected from the group consisting of methotrexate, abatacept,adalimumab, rituximab, etanercept, certolizumab, and golimumab. In otherembodiments, the autoimmune disease is Crohn's disease or ulcerativecolitis, and the therapeutic agent for the treatment of the autoimmunedisease that is not infliximab is selected from the group consisting ofadalimumab, certolizumab, natalizumab, ustekinumab, vedolizumab,azathioprine, cyclosporine, methotrexate, and mercaptopurin.

In one aspect, the present disclosure provides methods for treating acondition in a subject in need of infliximab therapy, comprising:administering a therapeutically effective amount of infliximab to thesubject, wherein the subject has a decreased risk of drug-induced liverinjury (DILI), wherein the subject's decreased risk of DILI isassociated with an absence of one or more genetic variations in thesubject, wherein the subject has been tested for a presence of the oneor more genetic variations with a genetic assay and has been identifiedas not having the one or more genetic variations, wherein the geneticvariation comprises at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof. In some embodiments, thegenetic variation comprises the HLA-B*39:01 allele. In some embodiments,the genetic assay comprises one or more of a polymerase chain reaction(PCR)-based approach, a direct sequencing approach, a next generation(NGS) approach and/or a direct HLA typing test. In some embodiments, thegenetic assay comprises obtaining a PCR-amplified genomic DNA sample ofthe biological sample from the subject, contacting under hybridizingconditions the genomic DNA with an oligonucleotide that specificallyhybridizes to HLA-B*039:01, and detecting the presence or absence ofHLA-B*039:01 in the sample. In some embodiments, the method comprisesobtaining a biological sample from the subject and performing thegenetic assay on the biological sample.

In one aspect, the present disclosure provides methods for treating asubject with infliximab, wherein the subject is in need of treatment foran autoimmune disease, the method comprising the steps of: (i)determining the subject's risk of developing DILI upon treatment withinfliximab by obtaining or having obtained the HLA profile of thesubject; and (ii) if the subject has a defined HLA profile, thenadministering infliximab to the subject in an amount of less than 5mg/kg, and if the subject does not have the HLA profile, thenadministering infliximab to the subject in an amount of 5 mg/kg or more.In some embodiments, the risk of DILI in a subject having the definedHLA profile is lower following administration of less than 5 mg/kginfliximab than it would be if the infliximab was administered in anamount of 5 mg/kg infliximab or more. In some embodiments, the definedHLA profile comprises at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof. In someembodiments, the methods comprise administering infliximab to thesubject in an amount of less than about 5 mg/kg, less than about 4.5mg/kg, less than about 4 mg/kg, less than about 3.5 mg/kg, less thanabout 3 mg/kg, less than about 2.5 mg/kg, less than about 2 mg/kg, lessthan about 1.5 mg/kg, less than about 1 mg/kg, less than about 0.5mg/kg, less than about 0.25 mg/kg, less than about 0.1 mg/kg, or less ifthe subject has the defined HLA profile. In some embodiments, themethods comprise administering 0 mg/kg infliximab to the subject if thesubject has the defined HLA profile. In some embodiments, the methodcomprises administering infliximab in an amount of 5 mg/kg or more ifthe subject does not have the defined HLA profile. In some embodiments,the risk of DILI in the subject having the defined HLA profile is lowerfollowing administration of less than about 5 mg/kg, less than about 4.5mg/kg, less than about 4 mg/kg, less than about 3.5 mg/kg, less thanabout 3 mg/kg, less than about 2.5 mg/kg, less than about 2 mg/kg, lessthan about 1.5 mg/kg, less than about 1 mg/kg, less than about 0.5mg/kg, less than about 0.25 mg/kg, less than about 0.1 mg/kg, or less ofinfliximab. In some embodiments, administration of 0 mg/kg infliximab tothe subject having an HLA profile comprising at least one HLA alleleselected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, reduces the risk of development of DILI inthe subject to the level of risk of a subject who does not have an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, the method comprising(i) determining if the subject has a defined HLA profile, and (ii)administering infliximab to the subject in an amount of less than 5mg/kg if the subject has the defined HLA profile. In some embodiments,the defined HLA profile comprises at least one HLA allele selected fromthe group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof. In some embodiments, the methods comprisedetermining if the subject has the defined HLA profile; andadministering infliximab to the subject in an amount of less than about5 mg/kg, less than about 4.5 mg/kg, less than about 4 mg/kg, less thanabout 3.5 mg/kg, less than about 3 mg/kg, less than about 2.5 mg/kg,less than about 2 mg/kg, less than about 1.5 mg/kg, less than about 1mg/kg, less than about 0.5 mg/kg, less than about 0.25 mg/kg, less thanabout 0.1 mg/kg, or less if the subject has the defined HLA profile, andadministering infliximab in an amount of 5 mg/kg or more if the subjectdoes not have the defined HLA profile. In such embodiments, the risk ofDILI in the subject having the defined HLA profile is lower followingadministration of less than about 5 mg/kg, less than about 4.5 mg/kg,less than about 4 mg/kg, less than about 3.5 mg/kg, less than about 3mg/kg, less than about 2.5 mg/kg, less than about 2 mg/kg, less thanabout 1.5 mg/kg, less than about 1 mg/kg, less than about 0.5 mg/kg,less than about 0.25 mg/kg, less than about 0.1 mg/kg, or less ofinfliximab.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, wherein the subject hasan HLA profile comprising at least one HLA allele selected from thegroup consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and wherein the method comprisesadministering to the subject infliximab at a dose of less than 5 mg/kgbody weight of infliximab. In further embodiments, the method comprisesadministering to the subject infliximab at a dose of less than about 5mg/kg, less than about 4.5 mg/kg, less than about 4 mg/kg, less thanabout 3.5 mg/kg, less than about 3 mg/kg, less than about 2.5 mg/kg,less than about 2 mg/kg, less than about 1.5 mg/kg, less than about 1mg/kg, less than about 0.5 mg/kg, less than about 0.25 mg/kg, less thanabout 0.1 mg/kg, or less. In yet further embodiments, the methodcomprises administering to the subject 0 mg/kg infliximab.

In one aspect, the present disclosure provides methods for treating asubject selected for treatment with infliximab, wherein the subject isin need of treatment for an autoimmune disease, wherein the subject hasan HLA profile comprising at least one HLA allele selected from thegroup consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof. In some embodiments, the method comprisesadministering to the subject infliximab at a dose of less than 5 mg/kgbody weight of infliximab. In further embodiments, the method comprisesadministering to the subject infliximab at a dose of less than about 5mg/kg, less than about 4.5 mg/kg, less than about 4 mg/kg, less thanabout 3.5 mg/kg, less than about 3 mg/kg, less than about 2.5 mg/kg,less than about 2 mg/kg, less than about 1.5 mg/kg, less than about 1mg/kg, less than about 0.5 mg/kg, less than about 0.25 mg/kg, less thanabout 0.1 mg/kg, or less. In further embodiments, the method comprisesadministering to the subject 0 mg/kg infliximab.

In some embodiments, the present disclosure provides methods fortreating a subject selected for treatment with infliximab, wherein thesubject has an HLA profile comprising at least one HLA allele selectedfrom the group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and wherein the method comprisesadministering infliximab to a subject having the HLA profile in anamount of less than 5 mg/kg and further comprising administering to thesubject an additional therapeutic agent. In further embodiments, themethod comprises administering to the subject infliximab at a dose ofless than about 5 mg/kg, less than about 4.5 mg/kg, less than about 4mg/kg, less than about 3.5 mg/kg, less than about 3 mg/kg, less thanabout 2.5 mg/kg, less than about 2 mg/kg, less than about 1.5 mg/kg,less than about 1 mg/kg, less than about 0.5 mg/kg, less than about 0.25mg/kg, less than about 0.1 mg/kg, or less, and an additional therapeuticagent. In further embodiments, the method comprises administering to thesubject 0 mg/kg infliximab and an additional therapeutic agent. In someembodiments, the additional therapeutic agent is selected from the groupconsisting of azathioprine, mercaptopurine, adalimumab, certolizumab,methotrexate, natalizumab, vedolizumab, ustekinumab, mesalamine,budesonide, hyoscyamine, celecoxib, hydroxychloroquin, etanercept,prednisone, cyclosporine, tocilizumab, meloxicam, leflunomide,sulfasalazine, abatacept, rituximab, golimumab, acitretin, secukinumab,apremilast, sarilumab, ixekizumab, and corticotropin. In particularembodiments, the additional therapeutic agent is selected from the groupconsisting of adalimumab, certolizumab, natalizumab, ustekinumab,vedolizumab, azathioprine, cyclosporine, methotrexate, mercaptopurin,etanercept, and rituximab. In some embodiments, the additionaltherapeutic agent is a TNF inhibitor that is not infliximab.

In some embodiments, the subject has rheumatoid arthritis, ankylosingspondylitis, or psoriatic arthritis, and the additional therapeuticagent is selected from the group consisting of methotrexate, abatacept,adalimumab, rituximab, etanercept, certolizumab, and golimumab. In otherembodiments, the subject has Crohn's disease or ulcerative colitis, andthe additional therapeutic agent is selected from the group consistingof adalimumab, certolizumab, natalizumab, ustekinumab, vedolizumab,azathioprine, cyclosporine, methotrexate, and mercaptopurin.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject selected for infliximab treatment,wherein the subject has an HLA profile comprising at least one HLAallele selected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and wherein the subject is treated byreducing the dose of infliximab to 0 mg/kg. In some embodiments, themethod reduces the risk of DILI in the subject. In some embodiments, themethod treats or prevents DILI in the subject.

In one aspect, the present disclosure provides methods for treating asubject for an autoimmune disease, wherein the subject was selected forinfliximab treatment, wherein the method comprises removingadministration of infliximab from the subject's treatment regimen,wherein the subject has an HLA profile comprising at least one HLAallele selected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof. In some embodiments, the method reduces therisk of DILI in the subject. In some embodiments, the method treats orprevents DILI in the subject.

In various embodiments provided herein, the present disclosure providesmethods for treating an autoimmune disease in a subject selected forinfliximab treatment and methods for treating a subject for anautoimmune disease wherein the subject was selected for infliximabtreatment, wherein the method comprises reducing the dose of infliximabto 0 mg/kg and/or wherein the method comprises removing administrationof infliximab from the subject's treatment regimen, wherein the methodfurther comprises administering to the subject a treatment selected fromthe group consisting of azathioprine, mercaptopurine, adalimumab,certolizumab, methotrexate, natalizumab, vedolizumab, ustekinumab,mesalamine, budesonide, hyoscyamine, celecoxib, hydroxychloroquin,etanercept, prednisone, cyclosporine, tocilizumab, meloxicam,leflunomide, sulfasalazine, abatacept, rituximab, golimumab, acitretin,secukinumab, apremilast, sarilumab, ixekizumab, and corticotropin. Inother embodiments, the method further comprises administering to thesubject a TNF inhibitor that is not infliximab.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, wherein the subject wasadministered infliximab and has exhibited symptoms of liver injury. Insome embodiments, the method comprises ceasing administration ofinfliximab, obtaining or having obtained the HLA profile of the subject,and selecting the subject for treatment with a therapeutic agent that isan alternative to infliximab if the subject has an HLA profilecomprising at least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof. In furtherembodiments, the alternative to infliximab is selected from the groupconsisting of azathioprine, mercaptopurine, adalimumab, certolizumab,methotrexate, natalizumab, vedolizumab, ustekinumab, mesalamine,budesonide, hyoscyamine, celecoxib, hydroxychloroquin, etanercept,prednisone, cyclosporine, tocilizumab, meloxicam, leflunomide,sulfasalazine, abatacept, rituximab, golimumab, acitretin, secukinumab,apremilast, sarilumab, and corticotropin. In some embodiments, thealternative to infliximab is a TNF inhibitor that is not infliximab. Insome embodiments, the method further comprises administering to thesubject an anti-inflammatory drug. For example, in some embodiments, themethod comprises administering a steroid to the subject.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, wherein the subject hasan HLA profile comprising at least one HLA allele selected from thegroup consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and wherein the subject is treated using anactive regimen comprising: (i) monitoring the subject for liver injury,and (ii) not administering infliximab to the subject. In furtherembodiments, the active regimen comprising monitoring for liver injurycomprises one or more of monitoring liver enzyme levels, monitoringserum bilirubin levels, monitoring the subject for jaundice, andmonitoring the subject for upper abdominal discomfort. In someembodiments, the subject is monitored for liver injury daily, everyother day, every two days, twice per week, weekly, every two weeks, ormonthly.

In various aspects of the present disclosure, the subject has an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof. Thus, thedisclosure is related to a particular patient population having at leastone HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof. In further embodiments, theHLA profile of the subject and/or patient population comprises acombination of two of the HLA alleles, or a combination of three of theHLA alleles, or a combination of four of the HLA alleles, or acombination of five or more of the HLA alleles.

In one aspect, the present disclosure provides a method for treatingpatients having an autoimmune disease with infliximab, wherein thepopulation excludes patients having an HLA profile comprising at leastone HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof. Thus, in some embodiments,the present disclosure provides a method of treating a population ofpatients having an autoimmune disease with infliximab, wherein themethod comprises excluding patients having an HLA profile comprising atleast one HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof, from the population ofpatients; and treating the population of patients with at least 1 mg/kg,at least 2 mg/kg, at least 3 mg/kg, at least 4 mg/kg, or at least 5mg/kg infliximab.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, wherein the subject hasbeen determined to have an HLA profile that does not include any HLAallele selected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*02:01,HLA-DRB1*07:01, HLA-DQB1*02:02, HLA-B*13:02, HLA-A*01:01, HLA-A*24:02,HLA-C*06:02, HLA-B*40:01, HLA-DPB1*04:01, HLA-DQB1*03:03, HLA-C*02:02,HLA-C*03:04, HLA-DRB1*11:01, HLA-DQA1*05:05, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-A*02:01, HLA-DQB1*03:01,HLA-A*03:01, HLA-DPB1*04:02, HLA-C*07:01, HLA-B*44:03, and HLA-C*05:01,wherein the method comprises administering infliximab to the subject.

In one aspect, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, the method comprising:(i) detecting whether the subject has an HLA profile that includes oneor more HLA alleles selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*02:01, HLA-DRB1*07:01, HLA-DQB1*02:02, HLA-B*13:02,HLA-A*01:01, HLA-A*24:02, HLA-C*06:02, HLA-B*40:01, HLA-DPB1*04:01,HLA-DQB1*03:03, HLA-C*02:02, HLA-C*03:04, HLA-DRB1*11:01,HLA-DQA1*05:05, HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01,HLA-A*02:01, HLA-DQB1*03:01, HLA-A*03:01, HLA-DPB1*04:02, HLA-C*07:01,HLA-B*44:03, and HLA-C*05:01; and (ii) administering infliximab to thesubject. In further embodiments, the methods comprise obtaining abiological sample from the subject prior to detecting the HLA profile ofthe subject. In further embodiments, the methods comprise determiningthat the subject does not have one or more HLA alleles selected from thegroup consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*02:01, HLA-DRB1*07:01,HLA-DQB1*02:02, HLA-B*13:02, HLA-A*01:01, HLA-A*24:02, HLA-C*06:02,HLA-B*40:01, HLA-DPB1*04:01, HLA-DQB1*03:03, HLA-C*02:02, HLA-C*03:04,HLA-DRB1*11:01, HLA-DQA1*05:05, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-A*02:01, HLA-DQB1*03:01, HLA-A*03:01,HLA-DPB1*04:02, HLA-C*07:01, HLA-B*44:03, and HLA-C*05:01. Thus, in someembodiments, the present disclosure provides methods for treating anautoimmune disease in a subject in need thereof, comprising: (i)obtaining a biological sample from the subject; (ii) detecting whetherthe subject has an HLA profile that includes one or more HLA allelesselected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*02:01,HLA-DRB1*07:01, HLA-DQB1*02:02, HLA-B*13:02, HLA-A*01:01, HLA-A*24:02,HLA-C*06:02, HLA-B*40:01, HLA-DPB1*04:01, HLA-DQB1*03:03, HLA-C*02:02,HLA-C*03:04, HLA-DRB1*11:01, HLA-DQA1*05:05, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-A*02:01, HLA-DQB1*03:01,HLA-A*03:01, HLA-DPB1*04:02, HLA-C*07:01, HLA-B*44:03, and HLA-C*05:01;(iii) determining that the subject does not have one or more HLA allelesselected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*02:01,HLA-DRB1*07:01, HLA-DQB1*02:02, HLA-B*13:02, HLA-A*01:01, HLA-A*24:02,HLA-C*06:02, HLA-B*40:01, HLA-DPB1*04:01, HLA-DQB1*03:03, HLA-C*02:02,HLA-C*03:04, HLA-DRB1*11:01, HLA-DQA1*05:05, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-A*02:01, HLA-DQB1*03:01,HLA-A*03:01, HLA-DPB1*04:02, HLA-C*07:01, HLA-B*44:03, and HLA-C*05:01,based on detecting the absence of said HLA alleles in step (ii); (iv)administering infliximab to the subject.

In some embodiments, the HLA profiles provided herein comprise at leastone HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, and HLA-C*03:03, or any combination thereof.

In further embodiments, the HLA profiles provided herein comprise atleast one HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof.

In some embodiments, the HLA profile of the subject and/or patientpopulation comprises HLA-B*39:01.

In some embodiments, the HLA profile of the subject and/or patientpopulation comprises a combination of two HLA alleles, wherein the2-allele combination is selected from the group consisting of:

HLA-B*07:02, HLA-DQA1*01:03,

HLA-C*07:02, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DQA1*01:03,

HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-DPB1*01:01, HLA-DQB1*02:01,

HLA-DPB1*01:01, HLA-DQA1*05:01, and

HLA-DPB1*01:01, HLA-DRB1*03:01.

In other embodiments, the HLA profile of the subject and/or patientpopulation comprises a combination of three HLA alleles, wherein the3-allele combination is selected from the group consisting of:

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-A*24:02, HLA-B*07:02, HLA-DQA1*01:03,

HLA-B*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*01:03,

HLA-C*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DQB1*03:01, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQB1*03:01, HLA-DRB1*13:01,

HLA-A*24:02, HLA-C*07:02, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQB1*03:01,

HLA-B*07:02, HLA-C*07:02, HLA-DQA1*01:03,

HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*02:01, HLA-C*03:03, HLA-DQA1*05:01,

HLA-A*02:01, HLA-C*03:03, HLA-DQB1*02:01,

HLA-A*02:01, HLA-C*03:03, HLA-DRB1*03:01,

HLA-A*02:01, HLA-A*24:02, HLA-DQA1*01:03,

HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DRB1*13:01,

HLA-A*02:01, HLA-DPB1*01:01, HLA-DQB1*02:01,

HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*03:01,

HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DQB1*06:03,

HLA-A*02:01, HLA-DPB1*01:01, HLA-DQA1*05:01, and

HLA-A*02:01, HLA-DPB1*01:01, HLA-DRB1*03:01.

In still other embodiments, the HLA profile of the subject and/orpatient population comprises a combination of three HLA alleles, whereinthe 3-allele combination is selected from the group consisting of:

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*03:01,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DRB1*13:01,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*06:03, HLA-DRB1*13:01, and

HLA-A*24:02, HLA-B*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03.

In some embodiments, the HLA profile of the subject and/or patientpopulation comprises a combination of the following HLA alleles:HLA-C*07:01, HLA-DQA1*05:01, HLA-DQB1*02:01, HLA-DRB1*03:01,HLA-B*08:01, and HLA-DPB1*01:01.

In some embodiments, the HLA profile of the subject and/or patientpopulation comprises a combination of the following HLA alleles:HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQB1*03:01, HLA-DQA1*03:03,HLA-DQB1*06:03, HLA-DRB1*13:01, and HLA-DRB1*04:01.

In some embodiments, the HLA profile of the subject and/or patientpopulation comprises a combination of the following HLA allelesHLA-DPB1*04:01, HLA-C*07:01, HLA-DQA1*05:01, HLA-DQB1*02:01,HLA-DRB1*03:01, HLA-A*01:01, HLA-B*08:01, and HLA-DPB1*01:01.

Accordingly, in some embodiments, the present disclosure providesmethods for identifying and treating a particular patient population asdefined herein. In some embodiments, the patient population is apopulation of subjects having the HLA profile provided herein, andsuffering from an autoimmune disease. In some embodiments, the patientpopulation is a population of subjects having the HLA profile providedherein, and suffers from an inflammatory disease. In some embodiments,the patient population is a population of subjects having the HLAprofile provided herein, and suffering from a disease or disorder forwhich infliximab may be administered as a therapeutic agent. In someembodiments, the patient population is a population of subjects who donot have the HLA profile provided herein. In some embodiments, thepopulation of patients is a population from which patients having theHLA profile provided herein have been excluded.

In some embodiments, the HLA profile is or has been obtained using apolymerase chain reaction (PCR)-based approach. In some embodiments, theHLA profile is or has been obtained by obtaining a PCR-amplified genomicDNA sample of a biological sample from the subject, contacting underhybridizing conditions the genomic DNA with an oligonucleotide thatspecifically hybridizes to at least one HLA allele of claim 1, anddetecting the presence of at least one HLA allele. In some embodiments,the HLA profile is or has been obtained using next-generation sequencingof the HLA locus.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the results of the single-allele analysis. P-value for eachallele detected (x-axis) is shown in log scale (y-axis).

FIG. 2 shows the results of the two-allele analysis. P-value for eachtwo-allele combination (x-axis) is shown in log scale (y-axis). Thetwo-allele combinations with statistical significance surviving the BHcorrection are indicated in the figure and in Table 2.

FIG. 3 shows the results of the three-allele analysis. The figure showseach three-allele combination having a statistical significance thatsurvived the BH correction. P-value for each three-allele combination(x-axis) is shown in log scale (y-axis).

FIG. 4 shows the results of the four-allele analysis. The figure showseach four-allele combination having a statistical significance thatsurvived the BH correction. P-value for each four-allele combination(x-axis) is shown in log scale (y-axis).

FIG. 5 shows a summary of the alleles with significant results in thecases vs. controls individual data sets.

DETAILED DESCRIPTION

The present disclosure is related to the inventors' discovery that DILIin subjects treated with infliximab is associated with particulargenetic variants. The present inventors discovered that a set of HLAalleles are present at significantly higher frequency in subjects thatexhibited DILI after administration of infliximab. Accordingly, thepresent disclosure provides improved methods for treatment of diseases(e.g., autoimmune diseases) with infliximab in a defined patientpopulation, and/or for reduction in the risk of DILI in the definedpatient population.

Definitions

As used herein, the term “about” refers to an amount somewhat more orless than the stated parameter value, for example plus or minus five orten percent of the object that “about” modifies, or as one of skill inthe art would recognize from the context (e.g., approximately 50% of theinterval between values). The term “about” also includes the valuereferenced. For example, a dose of about 1 mg includes 1 mg, as well asvalues somewhat below or above 1, such as 0.9 mg and 1.1 mg. As usedherein, “and/or” refers to and encompasses any and all possiblecombinations of one or more of the associated listed items, as well asthe lack of combinations when interpreted in the alternative (“or”).

As used herein, the term “patient” refers to a human. In someembodiments, the patient can be a male or a female. In some embodiments,the patient can be an adult, or a pediatric patient. The term “subject”is used interchangeably herein with “patient.” In some embodiments, thesubject is a human that has a disease or condition that may be treatedwith infliximab. In some embodiments, prior to being treated with orprescribed infliximab for treatment of the disease or condition, thesubject undergoes HLA testing. In other embodiments, a subject that hasalready been prescribed or begun treatment with infliximab undergoes HLAtesting.

As used herein, a “patient population” is a group of patients who may begrouped together by a defining characteristic. For example, in someembodiments, the patient population provided herein is a population ofpatients having an HLA profile provided herein. In further embodiments,the patient population provided herein has an HLA profile providedherein, and is suffering from, at risk for, undergoing treatment for, orbeing evaluated for treatment for, an autoimmune or inflammatorydisease. In some embodiments, the patient population provided herein hasan HLA profile provided herein, and has been treated with, has beenprescribed, has been considered for treatment with, may be treated with,or is being evaluated for treatment with, infliximab. In someembodiments, the patient population provided herein has an HLA profileprovided herein, and is suffering from a disease or disorder for whichinfliximab may be administered as a therapeutic agent. In otherembodiments, the patient population provided herein is a population fromwhich patients having a particular HLA profile have been excluded. Incertain embodiments, the patient population may have other definingcharacteristics relating to health status, age, sex, race, and/orethnicity.

As used herein, a “patient treated with infliximab” or a “patientselected for infliximab therapy” or a “patient previously on infliximab”and the like refers to a patient having an indication which was amenableto treatment with infliximab.

As used herein, a “therapeutically effective regimen” refers to atreatment regimen of a duration and dosage sufficient to treat a diseaseor condition for which a drug is prescribed.

As used herein, a “dose” refers to the dosage of a drug, such asinfliximab, for example, as indicated on the manufacture's FDA-approvedlabel for the relevant indication or indications. As used herein, theterm “dosing regimen” refers to the overall therapeutic regimen of adrug, such as infliximab. For example, a patient may be prescribed oradministered a reduced dose of infliximab, and/or a reduced dose overtime in a reduced dosing regimen. In some embodiments, the patient wouldnot be administered, or would, in the physician's prescribed dosingregimen, be advised not to take infliximab. In some embodiments, thepatient may have previously been prescribed or administered infliximab,and the administration of infliximab may be ceased temporarily orpermanently in accordance with the methods provided herein.

Drug-Induced Liver Injury (DILI)

The term “adverse drug reaction” or “ADR,” as used herein, refers to anundesired, unintended effect of a drug. ADRs can lead to severedisability or death in a subject.

Drug-induced liver injury (DILI) is one of the most common and seriousADRs, and can lead to product withdrawal post-approval. When severe,DILI causes acute liver failure, death, or a need to receive a livertransplantation for survival. In subjects with DILI, the injured cellsinclude hepatocytes, bile duct epithelial cells, and vascularendothelial cells of the hepatic sinusoids and intrahepatic venoussystem. DILI can be acute or chronic, with patients suffering from acuteDILI often exhibiting chronic DILI over time. The clinicalmanifestations of acute DILI may initially include varying elevations inthe level of hepatic biochemical indexes including serum aspartateaminotransferase (AST; also called serum glutamic oxaloacetictransaminase, or SGOT), alanine aminotransferase (ALT; also called serumglutamate pyruvate transaminase or SGPT), alkaline phosphatase (ALP),and gamma-glutamyl transferase (GGT). Some patients with acute DILI mayhave symptoms such as fatigue, decreased appetite, aversion to oilyfood, tender liver, and epigastric discomfort. Patients may also exhibitjaundice, light-colored feces, and pruritus. Some acute DILI patientsmay have allergic manifestations including fever, rashes, increasedeosinophils, and even aching pain in joints, which may be accompanied byother manifestations of extrahepatic organ damage. Some patients maydevelop into acute or subacute liver failure. Chronic DILI may presentas, for example and without limitation, chronic hepatitis, liverfibrosis, compensated and decompensated cirrhosis, autoimmune hepatitis(AIH)-like DILI, chronic intrahepatic cholestasis, vanishing bile ductsyndrome (VBDS), or a combination thereof. Patients may also presentwith sinusoidal obstruction syndrome (SOS)/hepatic veno-occlusivedisease (VOD) or liver tumors. SOS/VOD may appear acutely with ascites,jaundice, and hepatomegaly.

DILI may be detected by monitoring levels of biochemical markers ofliver function, such as AST, ALT, ALP, GGT, and bilirubin (TBil). Levelsof any combination of these that are ULN (upper limit of normal) mayindicate DILI. For example, DILI may be identified biochemically asreaching any of the following: (1) ALT≥5 ULN; (2) ALP≥2 ULN, especiallyin patients with elevated 5′-nucleotidase or GGT, and withoutbone-diseases-related ALP elevation; (3) ALT≥3 ULN and TBil≥2 ULN (see,e.g., Aithal G P, Watkins P B, Andrade R J. “Case definition andphenotype standardization in drug-induced liver injury.” Clin PharmacolTher. 2011; 89(6):806-815). In some patients, a liver biopsy may beneeded to determine the presence or extent of liver damage.

However, the monitoring of biochemical markers is often ineffective forreducing the risk of DILI in subjects receiving a therapeutic agent.When the drug cannot be predicted to cause liver injury in a particularpatient population, DILI often goes undetected until severe damageoccurs and/or progresses too fast to prevent severe damage. Thus, thereis a serious need for a clinically useful method for predicting andpreventing the development of DILI upon administration of a drug.

HLA Typing

As described herein, the present Applicants have found that certainclasses of patients, i.e., patients having one or more of the particularHLA alleles or sets of HLA alleles provided herein, are at increasedrisk of developing DILI upon administration of infliximab.

The human leukocyte antigen (HLA) system describes the genetic locusencoding, among other immune-related genes, the major histocompatibilitycomplex (MHC) proteins in humans. MHCs which are the proteinsresponsible for regulation of the immune system. HLA-A, HLA-B, and HLA-Care the three major antigen loci of MHC class I, which is the MHC classthat presents peptides present inside the cell to CD8+ T cells. HLA-DP,HLA-DR, HLA-DQ, HLA-DM, and HLA-DO are the major loci of MHC class II,which present antigens from outside the cell to CD4+ T cells. Withinthese loci are pairs of alpha and beta chains: HLA-DPA1, HLA-DPB1,HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQA1, HLA-DQA2,HLA-DQB1, HLA-DQB2, HLA-DMA, HLA-DMB, HLA-DOA, and HLA-DOB. The term“allele” refers herein to an alternative form of the gene at a givenlocus; alleles occupy the same locus on homologous chromosomes. Thus, anHLA allele is the specific allele present at a given HLA locus for anindividual patient. The term “genetic variation” may be used herein todescribe an HLA allele.

As used herein, “HLA typing” and the like refers to determining asubject's HLA profile, which is made up of the individual's HLA alleles.The HLA typing disclosed herein includes determining whether aparticular HLA allele or set of alleles is present or absent in thepatient. Various methods for HLA typing are known in the art, and anymethod for determining the presence or absence of HLA alleles can beused in the methods disclosed herein. HLA typing can be performed atlow, intermediate, or high resolution. Low resolution HLA typing refersto typing wherein the alleles are reported at the two-digit level. Anexample of a representation of an HLA allele at the two-digit level isHLA-DQA1*01. Low resolution HLA typing can be achieved using serologicalmethods. The standard method for serological HLA typing is themicro-lymphocytotoxicity assay, in which the lymphocytes of a subjectare tested against a panel of antisera or monoclonal antibodies whosespecificity for HLA has been previously characterized. Antibodies thatbind to the HLA molecules induce lysis in the presence of complement,and indicate which HLA molecules were present on the subject'slymphocytes.

DNA- or RNA-based typing directly determines the sequence, and canprovide intermediate or high resolution results. High resolution methodsare preferred, in some embodiments, because tight linkage disequilibriumbetween genes and the high degree of polymorphism present at the MHCloci can make it difficult to obtain useful information with lowerresolution methods. High resolution HLA typing may be achieved usingDNA- or RNA-based methods and can provide HLA reporting at thefour-digit level. An example of a representation of an HLA allele at thefour-digit level is HLA-DQA1*01:03. Such methods include, withoutlimitation, PCR-sequence-specific primer (SSP) typing, PCR-sequencespecific oligonucleotide (SSO) hybridization, direct sequencing,sequence based typing (SBT; e.g., Sanger sequence based method ofsequencing), next generation sequencing (NGS), and the like. PCR-SSPinvolves allele sequence-specific primer pairs that are designed toselectively amplify target sequences that are specific to a singleallele, with PCR performed in the presence of control primer pairsmatching non-allelic sequences present in the sample. PCR-SSO typinguses PCR target amplification, hybridization of PCR products to a panelof immobilized sequence-specific oligonucleotides on beads, anddetection of probe-bound amplification product. SBT is based on PCRtarget amplification, followed by sequencing of the PCR products anddata analysis. NGS is an approach that can be achieved using variousmethods, for example those discussed in Carapito et al., Human Immunol.77(2016) 1016-23. In principle, NGS is similar to Sanger-basedsequencing, in that the bases of a DNA fragment are identifiedsequentially from signals emitted as each fragment is resynthesized froma DNA template strand. NGS achieves this in a scaled-up manner byallowing millions of reactions to occur in parallel. Advantages of NGSinclude the ability to multiplex, that is, amplify and sequence multipleHLA genes in a single reaction. Those skilled in the art will appreciatethat various commercially available kits and analysis software can beused to HLA type a sample.

Intermediate resolution HLA typing refers to a situation wherefour-digit level typing has been completed, but there are severalpossibilities for the HLA present. For example, in PCR-SSP, the PCRprimers used may yield more than one possible genotype that anindividual may have, which may require additional testing withadditional combinations of primers and/or cloning and sequencing of theclones in order to obtain an unambiguous HLA type.

In some embodiments, methods for HLA typing and/or detection of HLAalleles are referred to as “genetic assays.” Genetic assays can be usedto detect the presence or absence of one or more genetic variations(e.g., one or more alleles). For example, in some embodiments, thepresent disclosure provides methods for treating a subject in need ofinfliximab therapy or in need of treatment for an autoimmune disease ordisorder, comprising testing the subject for the presence or absence ofone or more genetic variations, using a genetic assay. In someembodiments, the one or more genetic variations are selected from thegroup consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01. In particular embodiments, the geneticvariation comprises the HLA-B*39:01 allele.

In one aspect, the present inventors found that a particular HLA allelewas associated with the development of DILI after subjects wereadministered infliximab. The inventors undertook an extensivestatistical analysis of the HLA alleles present in samples from subjectswho experienced DILI following administration with infliximab, ascompared to samples from healthy subjects (i.e., subjects who receivedinfliximab and did not experience DILI) and found a statisticallysignificant increased risk of developing DILI associated withHLA-B*39:01.

In another aspect, the present inventors found that a particular set ofHLA alleles are associated with the development of DILI after subjectswere administered infliximab. More specifically, the inventors undertookan extensive statistical analysis of the HLA alleles present in samplesfrom subjects who experienced DILI following administration withinfliximab, as compared to samples from healthy subjects (i.e., subjectswho received infliximab and did not experience DILI). Each of the HLAprofiles identified as being at a statistically significantly increasedrisk of developing DILI included at least one of the following HLAalleles: HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01.

In addition, the inventors assessed whether any two-allele,three-allele, four-allele, or greater than four-allele combinationsexhibited a statistically significant increase in the risk of DILIfollowing infliximab administration. The two-allele combinations, wherethe presence of at least one of the following sets of two alleles in anindividual's HLA profile conferred statistically significant increase inthe risk of DILI, were:

HLA-B*07:02, HLA-DQA1*01:03,

HLA-C*07:02, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DQA1*01:03,

HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-DPB1*01:01, HLA-DQB1*02:01,

HLA-DPB1*01:01, HLA-DQA1*05:01, and

HLA-DPB1*01:01, HLA-DRB1*03:01.

The three-allele combinations, where the presence of at least one of thefollowing sets of three alleles in an individual's HLA profile conferredstatistically significant increase in the risk of DILI, were:

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-A*24:02, HLA-B*07:02, HLA-DQA1*01:03,

HLA-B*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*01:03,

HLA-C*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DQB1*03:01, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQB1*03:01, HLA-DRB1*13:01,

HLA-A*24:02, HLA-C*07:02, HLA-DQA1*01:03,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQB1*03:01,

HLA-B*07:02, HLA-C*07:02, HLA-DQA1*01:03,

HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*02:01, HLA-C*03:03, HLA-DQA1*05:01,

HLA-A*02:01, HLA-C*03:03, HLA-DQB1*02:01,

HLA-A*02:01, HLA-C*03:03, HLA-DRB1*03:01,

HLA-A*02:01, HLA-A*24:02, HLA-DQA1*01:03,

HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DRB1*13:01,

HLA-A*02:01, HLA-DPB1*01:01, HLA-DQB1*02:01,

HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*03:01,

HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DQB1*06:03,

HLA-A*02:01, HLA-DPB1*01:01, HLA-DQA1*05:01, and

HLA-A*02:01, HLA-DPB1*01:01, HLA-DRB1*03:01.

The four-allele combinations, where the presence of at least one of thefollowing sets of four alleles in an individual's HLA profile conferredstatistically significant increase in the risk of DILI, were:

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQA1*03:03,

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DQB1*06:03,\

HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*03:01,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DRB1*13:01,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*06:03,

HLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DRB1*13:01,

HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*06:03, HLA-DRB1*13:01, and

HLA-A*24:02, HLA-B*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03.

In addition, certain higher level associations were determined toexhibit a statistically significant increase in the risk of DILIfollowing infliximab administration. For example, the combination of thefollowing alleles significantly increased the risk of DILI: HLA-C*07:01,HLA-DQA1*05:01, HLA-DQB1*02:01, HLA-DRB1*03:01, HLA-B*08:01, andHLA-DPB1*01:01; HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQB1*03:01,HLA-DQA1*03:03, HLA-DQB1*06:03, HLA-DRB1*13:01, and HLA-DRB1*04:01; orHLA-DPB1*04:01, HLA-C*07:01, HLA-DQA1*05:01, HLA-DQB1*02:01,HLA-DRB1*03:01, HLA-A*01:01, HLA-B*08:01, and HLA-DPB1*01:01.

Infliximab

Infliximab is a mouse-human chimeric monoclonal antibody that binds tohuman tumor necrosis factor (TNF). Due to the importance of TNF ininflammatory processes, this inhibitory antibody has a potentanti-inflammatory effect. Infliximab has been approved for use in theUnited States for rheumatoid arthritis, ankylosing spondylitis,psoriatic arthritis, plaque psoriasis, Crohn's disease (adult andpediatric) and ulcerative colitis (adult and pediatric). Infliximab canbe indicated for the treatment of moderate to severe active rheumatoidarthritis in patients who have had inadequate response or tolerance tomethotrexate. Infliximab is also under clinical investigation for use invarious other diseases and disorders, including, but not limited to,sterile corneal melt, depression, bipolar depression (e.g., bipolar I/IIdepression), refractory intestinal Behcet's disease, Takayasu'sarteritis, dolichoectatic vertibrobasilar (DVB) aneurysms, refractoryidiopathic scleritis, graft versus host disease (GVHD), steroidrefractory acute graft versus host disease, macular edema, diabeticmacular edema, refractory polymyalgia rheumatic (PMR), chroroidalneovascularization, Kawasaki disease, melanoma, advanced melanoma,inflammatory skin disease, sarcoidosis, and anal fistulae.

Infliximab is marketed under the trade name REMICADE®, and the FDA andEuropean Medicines Agency (EMA) have also approved an infliximabbiosimilar, INFLECTRA®. Various other biosimilars are also approved insome countries outside the US and/or are in development worldwide.

The dosing for infliximab varies by indication, but generally isadministered intravenously at a dose of 5 mg/kg, and over several doses(e.g., at 1, 2, and 6 weeks, with a maintenance dose at 6 or 8 weekintervals thereafter). In some embodiments, a therapeutically effectiveamount of infliximab is at least 5 mg/kg infliximab. For some patients,the prescribed dose may be increased to 10 mg/kg. For some patients withrheumatoid arthritis, infliximab may be administered in conjunction withmethotrexate, and the prescribed dose of infliximab may be 3 mg/kg, withor without an increase to 10 mg/kg and/or a maintenance dose every 4, 6,or 8 weeks. Infliximab has been known to cause hepatotoxicity, and evensevere hepatic reactions that can be fatal or necessitate a livertransplant. Generally, when a patient receiving infliximab exhibitsjaundice and/or liver enzyme elevations, administration of infliximab isceased. For some patients, corticosteroid treatment is needed once liverinjury has presented. Subjects experiencing liver toxicity may beswitched to an alternative therapeutic agent, such as etanercept, orother alternatives to infliximab.

In certain aspects of the present disclosure, there are provided methodsfor treating an autoimmune disease or other disease or disorder that maybe amenable to treatment with infliximab; or methods for reducing therisk or severity of DILI in subjects having an autoimmune disease orother disease or disorder that may be amenable to treatment withinfliximab. The methods include reducing the dose of infliximab;prescribing a dose of infliximab that is lower than the dose on theapproved label or the previously prescribed or otherwise prescribeddose; ceasing administration of infliximab; and/or not administeringinfliximab to the subject, which includes administering an alternativeto infliximab. For example, in some embodiments, the methods providedherein comprise administering infliximab to the subject in an amount ofless than about 5 mg/kg, less than about 4.5 mg/kg, less than about 4mg/kg, less than about 3.5 mg/kg, less than about 3 mg/kg, less thanabout 2.5 mg/kg, less than about 2 mg/kg, less than about 1.5 mg/kg,less than about 1 mg/kg, less than about 0.5 mg/kg, less than about 0.25mg/kg, less than about 0.1 mg/kg, or less. In certain embodiments, theterm “less than” a given dosing level encompasses a dose of 0 mg/kg. Forexample, in some embodiments, a subject who is administered “less than 5mg/kg infliximab” is administered 0 mg/kg infliximab. Thus, in someembodiments, administration of “less than 5 mg/kg infliximab” and thelike includes non-administration of infliximab. In some embodiments, thesubjects who are administered a reduced dose of infliximab and/or arenot administered infliximab in accordance with the methods providedherein are administered an alternative drug to treat the disease ordisorder. Thus, in some embodiments, subjects are treated according tothe methods provided herein with a therapeutic agent for the treatmentof the autoimmune disease that is not infliximab. In some embodiments,the subject may be administered any drug known or suspected of treatingthe disease or disorder that the subject is suffering from. For example,in some embodiments, the subject is administered a cytokine inhibitorthat is not infliximab. For example, the subject may be administered aTNF inhibitor that is not infliximab. In some embodiments, the subjectis administered a drug or therapeutic agent that is not infliximab or isan alternative to infliximab, for example a drug or therapeutic agentselected from the group consisting of azathioprine, mercaptopurine,adalimumab, certolizumab, methotrexate, natalizumab, vedolizumab,ustekinumab, mesalamine, budesonide, hyoscyamine, celecoxib,hydroxychloroquin, etanercept, prednisone, cyclosporine, tocilizumab,meloxicam, leflunomide, sulfasalazine, abatacept, rituximab, golimumab,acitretin, secukinumab, apremilast, sarilumab, ixekizumab,corticotropin, olsalazine, balsalazide, tacrolimus, topiramate,cholestyramine, mycophenolate mofetil, dexamethasone, hydrocortisone,cromolyn, clonidine, diclofenac, naproxen, ibuprofen, aspirin,esomeprazole, tofacitinib, famotidine, nabumetone, etodolac,atorvastatin, anakinra, methylprednisone, triamcinolone, doxycycline,indomethacin, sulindac, tramadol, auranofin, misoprostol, ketoprofen,oxaprozin, piroxicam, salsalate, acetaminophen, hydrocodone,minocycline, alemtuzumab, flurbiprofen, cortisone, penicillamine,cyclophosphamide, diflunisal, fenoprofen, interferon gamma-1b,meclofenamate, phenytoin, tetracycline, tolmetin, hydroxyurea,betamethasone, calcipotriene, brodalumab, guselkumab, and tildrakizumab.In some embodiments, the therapeutic agent that is not infliximab orthat is an alternative to infliximab includes any salts, esters,biosimilars, and the like of the additional or alternative therapeuticagents provided herein. Other drugs that may treat the disease ordisorder from which the subject suffers will be apparent to one ofordinary skill in the art and are encompassed by the present disclosure.

Diseases and Disorders

In one aspect, the present disclosure provides methods for treating asubject having an autoimmune or inflammatory disease. Autoimmune orinflammatory diseases, in some embodiments, are selected from the groupconsisting of Crohn's disease, psoriasis (including plaque psoriasis),arthritis (including rheumatoid arthritis, psoriatic arthritis,osteoarthritis, or juvenile idiopathic arthritis), multiple sclerosis,ankylosing spondylitis, spondyloarthritis, inflammatory bowel diseases(IBD), ulcerative colitis, systemic lupus erythematosus, celiac disease,myasthenia gravis, type 1 narcolepsy, neuromyelitis optica,chorioretinopathy, pemphigus vulgaris, Behcet's disease,glomerulonephritis, type 1 diabetes mellitus, epidermolysis bullosa,Goodpasture Syndrome, uveitis, sepsis, neurodegenerative diseases,neuronal regeneration, spinal cord injury, primary and metastaticcancers, a respiratory disorder, asthma, allergic and nonallergicasthma, chronic obstructive pulmonary disease (COPD), a conditioninvolving airway inflammation, eosinophilia, fibrosis and excess mucusproduction, cystic fibrosis, pulmonary fibrosis, an atopic disorder,atopic dermatitis, urticaria, eczema, allergic rhinitis, allergicenterogastritis, liver cirrhosis, liver fibrosis, and scleroderma.

In certain embodiments, the patient has an autoimmune disease. In someembodiments, the patient has a disease or condition selected fromCrohn's disease, pediatric Crohn's disease, ulcerative colitis,pediatric ulcerative colitis, rheumatoid arthritis, ankylosingspondylitis, psoriatic arthritis, and plaque psoriasis.

In some embodiments, the patient has a disease or condition selectedfrom the group consisting of sterile corneal melt, depression, bipolardepression (e.g., bipolar I/II depression), major depressive disorder(MDD), refractory intestinal Behcet's disease, Takayasu's arteritis,dolichoectatic vertibrobasilar (DVB) aneurysms, refractory idiopathicscleritis, graft versus host disease, steroid refractory acute graftversus host disease, macular edema, diabetic macular edema, refractorypolymyalgia rheumatic (PMR), chroroidal neovascularization, Kawasakidisease, melanoma, advanced melanoma, inflammatory skin disease,sarcoidosis, and anal fistulae. In some embodiments, the patient is arecipient of an organ transplant such as a kidney transplant.

Methods

The present inventors surprisingly found that the risk of DILI uponadministration of infliximab is significantly higher in subjects havinga particular HLA allele or set of alleles. Thus, infliximab iscontraindicated in the patient populations provided herein. Thisinformation can be used in methods for drastically improving thetreatment of patients having diseases or disorders that may be indicatedfor treatment with infliximab. Patients can be HLA typed prior to orfollowing initiation of an infliximab dosing regimen, and based on thisinformation infliximab can be excluded from the patient's treatmentregimen, or the patient can be administered a reduced dose or reduceddosing regimen of infliximab, or the administration of infliximab can behalted, based on the HLA typing and using the methods provided herein.Thus, in certain embodiments, the present disclosure provides new andimproved methods for treating autoimmune diseases or other diseases thatmay be treated with infliximab; new and improved methods for reducingthe risk of DILI, and other related improved methods. In particularembodiments, the methods relate to a defined patient population havingan HLA profile provided herein.

In some embodiments, the present disclosure provides methods fortreating a disease or disorder that may be amenable to treatment withinfliximab. In further embodiments, the disclosure provides methods fortreating a disease or disorder that may be amenable to treatment withinfliximab in a subject and/or patient population having certain HLAalleles and/or combinations of alleles provided herein. In someembodiments, the present disclosure provides methods for treating anautoimmune disease. In further embodiments, the disclosure providesmethods for treating an autoimmune disease in a subject and/or patientpopulation having certain HLA alleles and/or combinations of allelesprovided herein. In some embodiments, the methods relating to treating adisease or disorder (e.g., an autoimmune disease) that may be amenableto treatment with infliximab comprise determining or obtaining the HLAprofile of a subject and, if the subject has an HLA profile comprisingat least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, then (i)not administering infliximab to the subject; (ii) administering lessthan about 5 mg/kg infliximab to the subject (e.g., administering lessthan about 4 mg/kg, less than about 3 mg/kg, less than about 2 mg/kg,less than about 1 mg/kg or 0 mg/kg infliximab), (iii) administering analternative to infliximab to the subject; (iv) administering infliximabto the subject at a reduced dosing level and/or frequency relative tothe level and/or frequency that infliximab would have otherwise beenadministered, and/or (v) closely monitoring the subject for signs orsymptoms of DILI.

In some embodiments, the present disclosure provides methods forreducing the risk of DILI. In further embodiments, the risk ofdeveloping DILI after administration of infliximab is high in subjectshaving certain HLA alleles and/or combinations of alleles providedherein, and the methods provided herein reduce the risk that the subjectwill develop DILI by providing a means for identifying the risk in agiven patient or a population of patients, and reducing the risk. Insome embodiments, the methods for reducing the risk of DILI in a subjectcomprise determining or obtaining the HLA profile of the subject and, ifthe subject has an HLA profile comprising at least one HLA alleleselected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, then reducing the risk of DILI by (i) notadministering infliximab to the subject; (ii) administering less thanabout 5 mg/kg infliximab to the subject (e.g., administering less thanabout 4 mg/kg, less than about 3 mg/kg, less than about 2 mg/kg, lessthan about 1 mg/kg or 0 mg/kg infliximab), (iii) administering analternative to infliximab to the subject; (iv) administering infliximabto the subject at a reduced dosing level and/or frequency relative tothe level and/or frequency that infliximab would have otherwise beenadministered, and/or (v) closely monitoring the subject for signs orsymptoms of DILI.

In some embodiments, the methods provided herein can be used to reducethe severity of DILI, and/or speed the time to recovery from DILI thathas occurred in a subject following administration of infliximab. Thus,in some embodiments, the present disclosure provides methods forreducing the severity of and/or speeding recovery from DILI in a subjectthat has received infliximab, comprising determining or obtaining theHLA profile of the subject and, if the subject has an HLA profilecomprising at least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, thenreducing the risk of DILI by (i) ceasing administration of infliximab tothe subject; (ii) reducing the dose of infliximab to less than about 5mg/kg (e.g., administering less than about 4 mg/kg, less than about 3mg/kg, less than about 2 mg/kg, less than about 1 mg/kg or 0 mg/kginfliximab), (iii) administering an alternative to infliximab to thesubject, (iv) closely monitoring the subject for signs or symptoms ofDILI, and/or (v) treating the subject with a steroid or other drugindicated for treatment of DILI.

Race and/or ethnicity may confer varied genetic susceptibility to DILI.Subjects having the HLA profiles provided herein may be grouped orclustered into certain races or ethnicities. In some embodiments, thepatient treated by the methods of the present disclosure can becharacterized by two or more of the characteristics described herein. Insome embodiments, the patient may have an HLA profile provided herein(e.g., at least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, and/or a two-, three-, four-, five-,six-, seven-, or eight-allele combination provided herein, along with anadvanced age and/or an underlying disease or infection such as infectionwith hepatitis B virus (HBV) and/or hepatitis C virus (HCV) and/or humanimmunodeficiency virus (HIV). In some embodiments, the patient may be ofadvanced age, a high BMI, or a low BMI.

In certain embodiments, an HLA profile comprising at least one HLAallele selected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof confers a heightened risk of DILI uponadministration of infliximab to a patient population. In someembodiments, infliximab is contraindicated in the patient populationhaving the HLA profile.

In certain embodiments, an HLA profile comprising at least one set oftwo-allele combinations selected from HLA-B*07:02 and HLA-DQA1*01:03;HLA-C*07:02 and HLA-DQA1*01:03; HLA-A*24:02 and HLA-DQA1*01:03;HLA-DQA1*03:03 and HLA-DRB1*13:01; HLA-DQA1*03:03 and HLA-DQB1*06:03;HLA-DQA1*01:03 and HLA-DQA1*03:03; HLA-DPB1*01:01 and HLA-DQB1*02:01;HLA-DPB1*01:01 and HLA-DQA1*05:01; and HLA-DPB1*01:01 and HLA-DRB1*03:01confers a heightened risk of DILI upon administration of infliximab to apatient population. In some embodiments, infliximab is contraindicatedin the patient population having the HLA profile comprising any of thetwo-allele combinations.

In certain embodiments, an HLA profile comprising at least one set ofthree-allele combinations selected from HLA-A*24:02, HLA-DQA1*01:03, andHLA-DQA1*03:03; HLA-A*24:02, HLA-DQA1*03:03, and HLA-DQB1*06:03;HLA-A*24:02, HLA-DQA1*03:03, and HLA-DRB1*13:01; HLA-A*24:02,HLA-B*07:02, and HLA-DQA1*01:03; HLA-B*07:02, HLA-DPB1*04:01, andHLA-DQA1*01:03; HLA-A*24:02, HLA-DPB1*04:01, and HLA-DQA1*01:03;HLA-C*07:02, HLA-DPB1*04:01, and HLA-DQA1*01:03; HLA-A*24:02,HLA-DQB1*03:01, and HLA-DQB1*06:03; HLA-A*24:02, HLA-DQB1*03:01, andHLA-DRB1*13:01; HLA-A*24:02, HLA-C*07:02, and HLA-DQA1*01:03;HLA-A*24:02, HLA-DQA1*01:03, and HLA-DQB1*03:01; HLA-B*07:02,HLA-C*07:02, and HLA-DQA1*01:03; HLA-DPB1*04:01, HLA-DQA1*01:03, andHLA-DQA1*03:03; HLA-DPB1*04:01, HLA-DQA1*03:03, and HLA-DRB1*13:01;HLA-DPB1*04:01, HLA-DQA1*03:03, and HLA-DQB1*06:03; HLA-A*02:01,HLA-C*03:03, and HLA-DQA1*05:01; HLA-A*02:01, HLA-C*03:03, andHLA-DQB1*02:01; HLA-A*02:01, HLA-C*03:03, and HLA-DRB1*03:01;HLA-A*02:01, HLA-A*24:02, and HLA-DQA1*01:03; HLA-DQA1*03:03,HLA-DQB1*03:01, and HLA-DRB1*13:01; HLA-A*02:01, HLA-DPB1*01:01, andHLA-DQB1*02:01; HLA-DQA1*01:03, HLA-DQA1*03:03, and HLA-DQB1*03:01;HLA-DQA1*03:03, HLA-DQB1*03:01, and HLA-DQB1*06:03; HLA-A*02:01,HLA-DPB1*01:01, and HLA-DQA1*05:01; and HLA-A*02:01, HLA-DPB1*01:01, andHLA-DRB1*03:01 confers a heightened risk of DILI upon administration ofinfliximab to a patient population. In some embodiments, infliximab iscontraindicated in the patient population having the HLA profilecomprising any of the three-allele combinations.

In certain embodiments, an HLA profile comprising at least one set ofthree-allele combinations selected from HLA-A*24:02, HLA-DPB1*04:01,HLA-DQA1*01:03, and HLA-DQA1*03:03; HLA-A*24:02, HLA-DPB1*04:01,HLA-DQA1*03:03, and HLA-DQB1*06:03; HLA-A*24:02, HLA-DPB1*04:01,HLA-DQA1*03:03, and HLA-DRB1*13:01; HLA-A*24:02, HLA-DQA1*01:03,HLA-DQA1*03:03, and HLA-DQB1*03:01; HLA-A*24:02, HLA-DQA1*03:03,HLA-DQB1*03:01, and HLA-DQB1*06:03; HLA-A*24:02, HLA-DQA1*03:03,HLA-DQB1*03:01, and HLA-DRB1*13:01; HLA-A*24:02, HLA-DQA1*01:03,HLA-DQA1*03:03, and HLA-DQB1*06:03; HLA-A*24:02, HLA-DQA1*01:03,HLA-DQA1*03:03, and HLA-DRB1*13:01; HLA-A*24:02, HLA-DQA1*03:03,HLA-DQB1*06:03, and HLA-DRB1*13:01; and HLA-A*24:02, HLA-B*07:02,HLA-DPB1*04:01, and HLA-DQA1*01:03 confers a heightened risk of DILIupon administration of infliximab to a patient population. In someembodiments, infliximab is contraindicated in the patient populationhaving the HLA profile comprising any of the four-allele combinations.

In some embodiments, an HLA profile comprising HLA-B*39:01 confers aheightened risk of DILI upon administration of infliximab to a patientor patient population.

In certain embodiments, an HLA profile comprising HLA-C*07:01,DQA1*05:01, DQB1*02:01, DRB1*03:01, B*08:01, and DPB1*01:01 confers aheightened risk of DILI upon administration of infliximab to a patientpopulation. In certain embodiments, an HLA profile comprisingHLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQB1*03:01, HLA-DQA1*03:03,HLA-DQB1*06:03, HLA-DRB1*13:01, and HLA-DRB1*04:01 confers a heightenedrisk of DILI upon administration of infliximab to a patient population.In certain embodiments, an HLA profile comprising HLA-DPB1*04:01,HLA-C*07:01, HLA-DQA1*05:01, HLA-DQB1*02:01, HLA-DRB1*03:01,HLA-A*01:01, HLA-B*08:01, and HLA-DPB1*01:01 confers a heightened riskof DILI upon administration of infliximab to a patient population.

In some embodiments, the present disclosure provides methods fortreating an autoimmune disease comprising administering less than 5mg/kg infliximab (e.g., 0 mg/kg infliximab) and alternatively oradditionally administering to the subject an alternative or additionaltherapeutic agent for the autoimmune disease, in a subject having an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof. In someembodiments, the present disclosure provides methods for treating anautoimmune disease comprising administering less than 5 mg/kg infliximab(e.g., 0 mg/kg infliximab) and alternatively or additionallyadministering to the subject an alternative or additional therapeuticagent for the autoimmune disease, in a subject having any of the two-three- or four-allele combinations provided herein. In some embodiments,the alternative or additional therapeutic agent is selected from thegroup consisting of azathioprine, mercaptopurine, adalimumab,certolizumab, methotrexate, natalizumab, vedolizumab, ustekinumab,mesalamine, budesonide, hyoscyamine, celecoxib, hydroxychloroquin,etanercept, prednisone, cyclosporine, tocilizumab, meloxicam,leflunomide, sulfasalazine, abatacept, rituximab, golimumab, acitretin,secukinumab, apremilast, sarilumab, ixekizumab, and corticotropin. Inparticular embodiments, the therapeutic agent that is not infliximab isselected from the group consisting of adalimumab, certolizumab,natalizumab, ustekinumab, vedolizumab, azathioprine, cyclosporine,methotrexate, mercaptopurin, etanercept, and rituximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is etanercept. Etanercept (ENBREL® and its biosimilars) isapproved by the FDA for treatment of rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, polyarticular juvenile idiopathicarthritis, and plaque psoriasis. Etanercept may be administered at adose of about 5 mg, about 10 mg, about 25 mg, about 50 mg, about 75 mg,or about 100 mg. Alternatively etanercept may be administered at a doseof about 0.5 mg/kg, about 0.8 mg/kg, about 1 mg/kg, about 5 mg/kg, orabout 10 mg/kg. Etanercept may be administered parenterally, such as bysubcutaneous injection. Patients receiving etanercept as an additionalagent or alternative to infliximab may receive, for example, a 50 mgsubcutaneous dose of etanercept, once weekly. In some embodiments, thepresent disclosure provides methods for treating an autoimmune diseasein a subject having an HLA profile defined herein (e.g., comprising atleast one HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01), wherein the method comprises administering etanerceptto the subject. In some embodiments, the subject has rheumatoidarthritis, psoriatic arthritis, ankylosing spondylitis, plaquepsoriasis, Crohn's disease (adult or pediatric), or ulcerative colitis(adult or pediatric). In some embodiments, the subject has an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, and thesubject is selected for infliximab therapy, but infliximab therapy isstopped, reduced, or never initiated, wherein the subject isadministered etanercept as an additional therapeutic agent or analternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is methotrexate. Methotrexate (TREXALL® and others) is approved bythe FDA for treatment of rheumatoid arthritis, polyarticular juvenileidiopathic arthritis, and psoriasis. Methotrexate may be administered ata dose of about 5 mg, about 7.5 mg, about 10 mg, about 15 mg, about 20mg, about 25 mg, about 30 mg, or about 50 mg. Methotrexate may beadministered orally or parenterally, such as by intramuscular,subcutaneous, or intravenous injection. In some embodiments, the presentdisclosure provides methods for treating an autoimmune disease in asubject having an HLA profile defined herein (e.g., comprising at leastone HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01), wherein the method comprises administering methotrexateto the subject. In some embodiments, the subject has rheumatoidarthritis, psoriatic arthritis, ankylosing spondylitis, plaquepsoriasis, Crohn's disease (adult or pediatric), or ulcerative colitis(adult or pediatric). In some embodiments, the subject has an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, and thesubject is selected for infliximab therapy, but infliximab therapy isstopped, reduced, or never initiated, wherein the subject isadministered methotrexate as an additional therapeutic agent or analternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is adalimumab. Adalimumab (HUMIRA® and its biosimilars) isapproved by the FDA for treatment of rheumatoid arthritis, juvenileidiopathic arthritis, psoriatic arthritis, ankylosing spondylitis,Crohn's disease, and plaque psoriasis. Adalimumab may be administered ata dose of about 20 mg, about 25 mg, about 30 mg, about 35 mg, about 40mg, about 50 mg, about 80 mg, about 120 mg, about 160 mg, or about 200mg. Adalimumab may be administered parenterally, such as byintramuscular, subcutaneous, or intravenous injection. In someembodiments, adalimumab may be administered by subcutaneous injection ofabout 40 mg every other week, or about 80 mg or about 160 mg as aninitial dose followed by 40 mg maintenance doses. In some embodiments,the present disclosure provides methods for treating an autoimmunedisease in a subject having an HLA profile defined herein (e.g.,comprising at least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01), wherein the method comprisesadministering adalimumab to the subject. In some embodiments, thesubject has rheumatoid arthritis, psoriatic arthritis, ankylosingspondylitis, plaque psoriasis, Crohn's disease (adult or pediatric), orulcerative colitis (adult or pediatric). In some embodiments, thesubject has an HLA profile comprising at least one HLA allele selectedfrom the group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and the subject is selected for infliximabtherapy, but infliximab therapy is stopped, reduced, or never initiated,wherein the subject is administered adalimumab as an additionaltherapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is abatacept. Abatacept (ORENCIA® and its biosimilars) is approvedby the FDA for treatment of rheumatoid arthritis and juvenile idiopathicarthritis. Abatacept may be administered at a dose of about 10 mg/kg, orabout 100 mg, about 250 mg, about 500 mg, about 750 mg, or about 1000mg. Abatacept may be administered parenterally, such as byintramuscular, subcutaneous, or intravenous injection. In someembodiments, abatacept may be administered via an intravenous loadingdose followed by intravenous or subcutaneous dosing thereafter. In someembodiments, abatacept is administered weekly. In some embodiments, thepresent disclosure provides methods for treating an autoimmune diseasein a subject having an HLA profile defined herein (e.g., comprising atleast one HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01), wherein the method comprises administering abatacept tothe subject. In some embodiments, the subject has rheumatoid arthritis,psoriatic arthritis, ankylosing spondylitis, plaque psoriasis, Crohn'sdisease (adult or pediatric), or ulcerative colitis (adult orpediatric). In some embodiments, the subject has an HLA profilecomprising at least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, and thesubject is selected for infliximab therapy, but infliximab therapy isstopped, reduced, or never initiated, wherein the subject isadministered abatacept as an additional therapeutic agent or analternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is rituximab. Rituximab (RITUXAN® and its biosimilars) is approvedby the FDA for treatment of leukemia, lymphoma, and rheumatoidarthritis. Rituximab may be administered in a dose of about 250 mg/m2,about 275 mg/m2, or about 500 mg/m2; or a dose of about 500 mg, about1000 mg, or about 1500 mg. Rituximab may be administered to rheumatoidarthritis patients in combination with methotrexate. Rituximab may beadministered to rheumatoid arthritis patients in courses of two 1000 mginfusions, each course separated by 16, 18, 20, 22, 24, or more weeks.Rituximab may be administered parenterally, such as by intramuscular,subcutaneous, or intravenous injection. In some embodiments, the presentdisclosure provides methods for treating an autoimmune disease in asubject having an HLA profile defined herein (e.g., comprising at leastone HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01), wherein the method comprises administering rituximab tothe subject. In some embodiments, the subject has rheumatoid arthritis,psoriatic arthritis, ankylosing spondylitis, plaque psoriasis, Crohn'sdisease (adult or pediatric), or ulcerative colitis (adult orpediatric). In some embodiments, the subject has an HLA profilecomprising at least one HLA allele selected from the group consisting ofHLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, and thesubject is selected for infliximab therapy, but infliximab therapy isstopped, reduced, or never initiated, wherein the subject isadministered rituximab as an additional therapeutic agent or analternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is certolizumab. Certolizumab (CIMZIA® and its biosimilars) isapproved by the FDA for treatment of rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, and Crohn's disease. Certolizumab maybe administered in a dose of about 100 mg, about 200 mg, about 300 mg,about 400 mg, or about 500 mg. In some embodiments, certolizumab may beadministered at a dose of 400 mg, administered in two subcutaneousinjections of 200 mg. In some embodiments, an initial 400 mg dose isfollowed by doses of 200 mg or 400 mg weekly or every other week afterthe initial dose. Certolizumab may be administered parenterally, such asby intramuscular, subcutaneous, or intravenous injection. In someembodiments, the present disclosure provides methods for treating anautoimmune disease in a subject having an HLA profile defined herein(e.g., comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01), wherein the method comprisesadministering certolizumab to the subject. In some embodiments, thesubject has rheumatoid arthritis, psoriatic arthritis, ankylosingspondylitis, plaque psoriasis, Crohn's disease (adult or pediatric), orulcerative colitis (adult or pediatric). In some embodiments, thesubject has an HLA profile comprising at least one HLA allele selectedfrom the group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and the subject is selected for infliximabtherapy, but infliximab therapy is stopped, reduced, or never initiated,wherein the subject is administered certolizumab as an additionaltherapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is golimumab. Golimumab (SIMPONI® and its biosimilars) is approvedby the FDA for treatment of rheumatoid arthritis, psoriatic arthritis,and ankylosing spondylitis. Golimumab may be administered in a dose ofabout 10 mg, about 25 mg, about 50 mg, or about 100 mg. In someembodiments, golimumab may be administered at a dose of about 50 mg onceper month by subcutaneous injection. Golimumab may be administeredparenterally, such as by intramuscular, subcutaneous, or intravenousinjection. In some embodiments, the present disclosure provides methodsfor treating an autoimmune disease in a subject having an HLA profiledefined herein (e.g., comprising at least one HLA allele selected fromthe group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01),wherein the method comprises administering golimumab to the subject. Insome embodiments, the subject has rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, plaque psoriasis, Crohn's disease(adult or pediatric), or ulcerative colitis (adult or pediatric). Insome embodiments, the subject has an HLA profile comprising at least oneHLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof, and the subject is selectedfor infliximab therapy, but infliximab therapy is stopped, reduced, ornever initiated, wherein the subject is administered golimumab as anadditional therapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is natalizumab. Natalizumab (TYSABRI® and its biosimilars) isapproved by the FDA for treatment of Crohn's disease and multiplesclerosis. Natalizumab may be administered in a dose of about 300 mg.Natalizumab may be administered parenterally, such as by intramuscular,subcutaneous, or intravenous injection. In some embodiments, natalizumabmay be administered to subjects by intravenous infusion of about 300 mgonce per month. In some embodiments, the present disclosure providesmethods for treating an autoimmune disease in a subject having an HLAprofile defined herein (e.g., comprising at least one HLA alleleselected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01),wherein the method comprises administering natalizumab to the subject.In some embodiments, the subject has rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, plaque psoriasis, Crohn's disease(adult or pediatric), or ulcerative colitis (adult or pediatric). Insome embodiments, the subject has an HLA profile comprising at least oneHLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof, and the subject is selectedfor infliximab therapy, but infliximab therapy is stopped, reduced, ornever initiated, wherein the subject is administered natalizumab as anadditional therapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is ustekinumab. Ustekinumab (STELARA® and its biosimilars) isapproved by the FDA for treatment of Crohn's disease, plaque psoriasis,and psoriatic arthritis. Ustekinumab. may be administered in a dose ofabout 45 mg, about 90 mg, about 260 mg, about 390 mg, or about 520 mg.Ustekinumab may be administered parenterally, such as by intramuscular,subcutaneous, or intravenous injection. In some embodiments, ustekinumabmay be administered to subjects by subcutaneous administration every 4weeks, every 8 weeks or every 12 weeks; or by intravenous infusionfollowed by subcutaneous doses. In some embodiments, the presentdisclosure provides methods for treating an autoimmune disease in asubject having an HLA profile defined herein (e.g., comprising at leastone HLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01), wherein the method comprises administering ustekinumabto the subject. In some embodiments, the subject has rheumatoidarthritis, psoriatic arthritis, ankylosing spondylitis, plaquepsoriasis, Crohn's disease (adult or pediatric), or ulcerative colitis(adult or pediatric). In some embodiments, the subject has an HLAprofile comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01, or any combination thereof, and thesubject is selected for infliximab therapy, but infliximab therapy isstopped, reduced, or never initiated, wherein the subject isadministered ustekinumab as an additional therapeutic agent or analternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is vedolizumab. Vedolizumab (ENTYVIO® and its biosimilars) isapproved by the FDA for treatment of Crohn's disease and ulcerativecolitis. Vedolizumab may be administered in a dose of about 300 mg.Vedolizumab may be administered parenterally, such as by intramuscular,subcutaneous, or intravenous injection. In some embodiments, vedolizumabmay be administered to subjects by intravenous infusion, for example atinitial dosing and two and six weeks after the initial dosing, and/orevery 8 weeks thereafter. In some embodiments, the present disclosureprovides methods for treating an autoimmune disease in a subject havingan HLA profile defined herein (e.g., comprising at least one HLA alleleselected from the group consisting of HLA-B*39:01, HLA-C*12:03,HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01),wherein the method comprises administering vedolizumab to the subject.In some embodiments, the subject has rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, plaque psoriasis, Crohn's disease(adult or pediatric), or ulcerative colitis (adult or pediatric). Insome embodiments, the subject has an HLA profile comprising at least oneHLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof, and the subject is selectedfor infliximab therapy, but infliximab therapy is stopped, reduced, ornever initiated, wherein the subject is administered vedolizumab as anadditional therapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is azathioprine. Azathioprine (IMURAN® and others) is used fortreatment of rheumatoid arthritis and other autoimmune diseases.Azathioprine may be administered orally in a dose of about 0.5 mg/kg,about 1 mg/kg, about 1.5 mg/kg, about 2 mg/kg, or about 2.5 mg/kg.Azathioprine may be administered orally, such as an oral daily dose. Insome embodiments, the present disclosure provides methods for treatingan autoimmune disease in a subject having an HLA profile defined herein(e.g., comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01), wherein the method comprisesadministering azathioprine to the subject. In some embodiments, thesubject has rheumatoid arthritis, psoriatic arthritis, ankylosingspondylitis, plaque psoriasis, Crohn's disease (adult or pediatric), orulcerative colitis (adult or pediatric). In some embodiments, thesubject has an HLA profile comprising at least one HLA allele selectedfrom the group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and the subject is selected for infliximabtherapy, but infliximab therapy is stopped, reduced, or never initiated,wherein the subject is administered azathioprine as an additionaltherapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is cyclosporine. Cyclosporine (NEORAL® and others) is approved bythe FDA for treatment of rheumatoid arthritis and psoriasis.Cyclosporine may be administered at a dose of about 1 mg/kg, about 1.5mg/kg, about 1.75 mg/g, about 2 mg/kg, about 3 mg/kg, about 3.5 mg/kg,or about 4 mg/kg. Cyclosporine may be administered orally orparenterally. For example, cyclosporine may be administered orally twiceper day. In some embodiments, the present disclosure provides methodsfor treating an autoimmune disease in a subject having an HLA profiledefined herein (e.g., comprising at least one HLA allele selected fromthe group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01),wherein the method comprises administering cyclosporine to the subject.In some embodiments, the subject has rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, plaque psoriasis, Crohn's disease(adult or pediatric), or ulcerative colitis (adult or pediatric). Insome embodiments, the subject has an HLA profile comprising at least oneHLA allele selected from the group consisting of HLA-B*39:01,HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02, HLA-DQA1*03:03,HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03,HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01,HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01,HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, andHLA-DRB1*04:01, or any combination thereof, and the subject is selectedfor infliximab therapy, but infliximab therapy is stopped, reduced, ornever initiated, wherein the subject is administered cyclosporine as anadditional therapeutic agent or an alternative to infliximab.

In some embodiments, the alternative to infliximab and/or thetherapeutic agent that is not infliximab and/or additional therapeuticagent is mercaptopurin. Mercaptopurin is used for the treatment ofCrohn's disease and ulcerative colitis. Mercaptopurin may beadministered at a dose of about 0.5 mg/kg, 1 mg/kg, about 1.5 mg/kg,about 1.75 mg/g, about 2 mg/kg, about 3 mg/kg, about 3.5 mg/kg, or about4 mg/kg. Mercaptopurin may be administered orally or parenterally. Forexample, mercaptopurin may be administered orally twice per day. In someembodiments, the present disclosure provides methods for treating anautoimmune disease in a subject having an HLA profile defined herein(e.g., comprising at least one HLA allele selected from the groupconsisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01, HLA-DPB1*04:02,HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02, HLA-C*07:02, HLA-A*24:02,HLA-DQA1*03:03, HLA-DRB1*13:01, HLA-DQB1*06:03, HLA-DPB1*01:01,HLA-DQB1*02:01, HLA-DQA1*05:01, HLA-DRB1*03:01, HLA-DPB1*04:01,HLA-DQB1*03:01, HLA-A*02:01, HLA-C*03:03, HLA-C*07:01, HLA-A*01:01,HLA-B*08:01, and HLA-DRB1*04:01), wherein the method comprisesadministering mercaptopurin to the subject. In some embodiments, thesubject has rheumatoid arthritis, psoriatic arthritis, ankylosingspondylitis, plaque psoriasis, Crohn's disease (adult or pediatric), orulcerative colitis (adult or pediatric). In some embodiments, thesubject has an HLA profile comprising at least one HLA allele selectedfrom the group consisting of HLA-B*39:01, HLA-C*12:03, HLA-DQA1*03:01,HLA-DPB1*04:02, HLA-DQA1*03:03, HLA-DQA1*01:03, HLA-B*07:02,HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01,HLA-C*03:03, HLA-C*07:01, HLA-A*01:01, HLA-B*08:01, and HLA-DRB1*04:01,or any combination thereof, and the subject is selected for infliximabtherapy, but infliximab therapy is stopped, reduced, or never initiated,wherein the subject is administered mercaptopurin as an additionaltherapeutic agent or an alternative to infliximab.

All documents, including patents, applications, and non-patentpublications cited herein are incorporated herein in their entiretiesfor all purposes.

EXAMPLES Example 1. HLA Analysis of Patients with ADR Following Exposureto Infliximab

A set of 12 samples from subjects that had been treated with infliximaband had experienced drug-induced liver injury (DILI) (hereinafterreferred to as “diseased samples”) were HLA tested and compared to a setof 10,397 healthy control samples (hereinafter referred to as “healthysamples”). The healthy samples were obtained from a general populationof human subjects who did not experience DILI, and who may or may nothave been exposed to infliximab. Analysis of a patient's genomic HLAprofile and a robust statistical analysis was performed to identify HLAalleles and/or sets of alleles that are risk factors for the developmentof DILI following infliximab exposure.

In the first analysis of the infliximab samples, the inventors sought tofind if the proportion of diseased samples exposed to an allele variedsignificantly from the proportion of the healthy samples with thatallele. In order to do so, for each allele in the dataset (192 total),the inventors calculated the number of diseased samples present for anallele (a below), the number of diseased samples absent for the allele(c), the number of healthy samples present for the allele (b), and thenumber of healthy samples absent for the allele (d) (Table 1). Presencewas defined as being either homozygous or heterozygous for an allele inquestion. A two-sided Fisher's Exact Test (FET) was performed on thedata to calculate p-values.

TABLE 1 Set-up of analysis Diseased Healthy Allele Present a b AlleleAbsent c d

The results from the single allele analysis are provided in FIG. 1,which lists each allele's p-value on a logarithmic scale.

The results of the FET yielded three p-values below the standard 0.05significance threshold. In order to account for the high number ofhypotheses tested (192 total), the inventors then performed theBenjamini-Hochberg (BH) correction procedure for multiple comparisons.As this is an initial screening for potentially significant allele-druginteractions with a relatively small sample size, the false discoveryrate (Q) was set to twenty percent, or 0.2.

In the second analysis of the infliximab samples, the inventors soughtto find two-allele combinations that varied significantly in thediseased samples as compared to the healthy samples. In order to avoidtesting unrealistic or extremely doubtful hypotheses, the inventors onlytested for combinations in which each allele appeared at least threetimes individually (that is, they were present in at least 25% of thediseased samples). Likewise, only homozygous combinations that appearedat least three times were tested. These criteria dramatically reducedthe number of hypotheses tested, from 36,864 to 211. Once again, theinventors invoked the BH procedure with Q equal to 0.2 in order toaccount for the amount of hypotheses tested, which reduced the number ofsignificant results from 33 to 9. FIG. 2 is a plot of significanttwo-allele combinations, with those surviving BH-correction indicated.

Table 2. is the corresponding table showing the FET p-value, odds ratio(OR), and Benjamini Hochberg critical value, (i/m)Q, for theBH-significant two-allele combinations.

TABLE 2 Two-allele combinations Combination P-value OR (i/m)QHLA-B*07:02, HLA-DQA1*01:03 1.69E−03 15.92 9.48E−04 HLA-C*07:02,HLA-DQA1*01:03 2.37E−03 14.09 1.90E−03 HLA-A*24:02, HLA-DQA1*01:032.90E−03 13.09 2.84E−03 HLA-DQA1*03:03, HLA-DRB1*13:01 4.41E−03 23.933.79E−03 HLA-DQA1*03:03, HLA-DQB1*06:03 4.51E−03 23.66 4.74E−03HLA-DQA1*01:03, HLA-DQA1*03:03 4.71E−03 23.12 5.69E−03 HLA-DPB1*01:01,HLA-DQB1*02:01 6.86E−03 6.85 6.64E−03 HLA-DPB1*01:01, HLA-DQA1*05:016.97E−03 6.82 7.58E−03 HLA-DPB1*01:01, HLA-DRB1*03:01 7.04E−03 6.808.53E−03

In the third analysis of the infliximab samples, the inventors sought tofind three-allele combinations that varied significantly in the diseasedsamples as compared to the healthy samples. As with the two-allelecombinations, the inventors only tested for combinations in which eachallele appeared in at least 25% of our diseased samples. In addition toa frequency threshold, the inventors only sought combinations that werebiologically possible. Thus any combinations with more than two allelesper locus were removed. These criteria dramatically reduced the numberof hypotheses tested, from 1,216,480 to 1,336. Again the inventorsinvoked the BH procedure with Q equal to 0.2 in order to account for theamount of hypotheses tested, which reduced the number of significantresults from 152 to 25. FIG. 3 is a plot of BH-significant three-allelecombinations, and Table 3. provides the corresponding combination name,p-value, odds ratio, and Benjamini-Hochberg critical value

TABLE 3 Three-allele combinations Combination P-value OR (i/m)QHLA-A*24:02, HLA-DQA1*01:03, HLA-DQA1*03:03 1.27E−04 157.88 1.50E−04HLA-A*24:02, HLA-DQA1*03:03, HLA-DQB1*06:03 1.27E−04 157.88 2.99E−04HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01 1.45E−04 146.62 4.49E−04HLA-A*24:02, HLA-B*07:02, HLA-DQA1*01:03 6.31E−04 66.55 5.99E−04HLA-B*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03 6.70E−04 22.14 7.49E−04HLA-A*24:02, HLA-DPB1*04:01, HLA-DQA1*01:03 8.89E−04 20.03 8.98E−04HLA-C*07:02, HLA-DPB1*04:01, HLA-DQA1*01:03 9.34E−04 19.67 1.05E−03HLA-A*24:02, HLA-DQB1*03:01, HLA-DQB1*06:03 1.02E−03 51.56 1.20E−03HLA-A*24:02, HLA-DQB1*03:01, HLA-DRB1*13:01 1.12E−03 49.11 1.35E−03HLA-A*24:02, HLA-C*07:02, HLA-DQA1*01:03 1.28E−03 45.88 1.50E−03HLA-A*24:02, HLA-DQA1*01:03, HLA-DQB1*03:01 1.33E−03 44.87 1.65E−03HLA-B*07:02, HLA-C*07:02, HLA-DQA1*01:03 1.62E−03 16.15 1.80E−03HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQA1*03:03 2.01E−03 36.20 1.95E−03HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DRB1*13:01 2.08E−03 35.56 2.10E−03HLA-DPB1*04:01, HLA-DQA1*03:03, HLA-DQB1*06:03 2.15E−03 34.95 2.25E−03HLA-A*02:01, HLA-C*03:03, HLA-DQA1*05:01 2.43E−03 32.73 2.40E−03HLA-A*02:01, HLA-C*03:03, HLA-DQB1*02:01 2.43E−03 32.73 2.54E−03HLA-A*02:01, HLA-C*03:03, HLA-DRB1*03:01 2.43E−03 32.73 2.69E−03HLA-A*02:01, HLA-A*24:02, HLA-DQA1*01:03 3.40E−03 27.45 2.84E−03HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DRB1*13:01 3.49E−03 27.09 2.99E−03HLA-A*02:01, HLA-DPB1*01:01, HLA-DQB1*02:01 3.54E−03 12.17 3.14E−03HLA-DQA1*01:03, HLA-DQA1*03:03, HLA-DQB1*03:01 3.57E−03 26.73 3.29E−03HLA-DQA1*03:03, HLA-DQB1*03:01, HLA-DQB1*06:03 3.57E−03 26.73 3.44E−03HLA-A*02:01, HLA-DPB1*01:01, HLA-DQA1*05:01 3.57E−03 12.12 3.59E−03HLA-A*02:01, HLA-DPB1*01:01, HLA-DRB1*03:01 3.61E−03 12.08 3.74E−03

In the fourth analysis of the infliximab samples, the inventors soughtto find four-allele combinations that varied significantly in thediseased samples as compared to the healthy samples. The criteria forthis level of analysis were identical to the three-allele analysis.These criteria dramatically reduced the number of hypotheses tested,from 59,570,608 to 5,931. Again the inventors invoked the BH procedurewith Q equal to 0.2 in order to account for the amount of hypothesestested, which reduced the number of significant results from 399 to 10.FIG. 4 is a plot of BH-significant four-allele combinations, and Table4. below is the corresponding table containing the allele combination,p-value, odds ratio, and Benjamini-Hochberg critical value.

TABLE 4 Four-allele combinations Combination P-value OR (i/m)QHLA-A*24:02, HLA-DPB1*04:01, 5.45E−05 256.06 3.37E−05 HLA-DQA1*01:03,HLA-DQA1*03:03 HLA-A*24:02, HLA-DPB1*04:01, 5.45E−05 256.06 6.74E−05HLA-DQA1*03:03, HLA-DQB1*06:03 HLA-A*24:02, HLA-DPB1*04:01, 6.66E−05227.32 1.01E−04 HLA-DQA1*03:03, HLA-DRB1*13:01 HLA-A*24:02,HLA-DQA1*01:03, 9.44E−05 186.50 1.35E−04 HLA-DQA1*03:03, HLA-DQB1*03:01HLA-A*24:02, HLA-DQA1*03:03, 9.44E−05 186.50 1.69E−04 HLA-DQB1*03:01,HLA-DQB1*06:03 HLA-A*24:02, HLA-DQA1*03:03, 1.10E−04 171.48 2.02E−04HLA-DQB1*03:01, HLA-DRB1*13:01 HLA-A*24:02, HLA-DQA1*01:03, 1.27E−04157.88 2.36E−04 HLA-DQA1*03:03, HLA-DQB1*06:03 HLA-A*24:02,HLA-DQA1*01:03, 1.27E−04 157.88 2.70E−04 HLA-DQA1*03:03, HLA-DRB1*13:01HLA-A*24:02, HLA-DQA1*03:03, 1.27E−04 157.88 3.03E−04 HLA-DQB1*06:03,HLA-DRB1*13:01 HLA-A*24:02, HLA-B*07:02, 3.04E−04 97.81 3.37E−04HLA-DPB1*04:01, HLA-DQA1*01:03

A total of 14 different alleles were identified as present in at leastone of the combination analyses. The alleles are: HLA-DQA1*01:03,HLA-B*07:02, HLA-C*07:02, HLA-A*24:02, HLA-DQA1*03:03, HLA-DRB1*13:01,HLA-DQB1*06:03, HLA-DPB1*01:01, HLA-DQB1*02:01, HLA-DQA1*05:01,HLA-DRB1*03:01, HLA-DPB1*04:01, HLA-DQB1*03:01, HLA-A*02:01, andHLA-C*03:03. In the two-, three-, and four-allele combinations analyses,each of these identified alleles appeared in at least three of thecombination sets.

Following the four-allele analysis, we used inspection to search forpotential higher-level associations. During this analysis we discoveredthree combinations that exhibited an increase in frequency in thediseased samples. The first combination included the following alleles:HLA-DPB1*04:01, HLA-C*07:01, HLA-DQA1*05:01, HLA-DQB1*02:01,HLA-DRB1*03:01, HLA-A*01:01, HLA-B*08:01, and HLA-DPB1*01:01. Out of the12 diseased samples, two individuals (16.7%) had this eight-allelecombination while 199 of the 10397 (1.91%) healthy samples had it. Thisresulted in a FET p-value of 2.16E-02 with an OR of 10.24 (95% CI1.08-48.52). The next combination we investigated included the followingalleles: HLA-DPB1*04:01, HLA-DQA1*01:03, HLA-DQB1*03:01, HLA-DQA1*03:03,HLA-DQB1*06:03, HLA-DRB1*13:01, and HLA-DRB1*04:01. Two diseased samples(16.7%) had this combination, and only 43 healthy samples (0.41%), whichresulted in a p-value of 1.17E-03 and OR of 47.95 (95% CI 4.97-234.85).Lastly, we investigated the following six-allele combination, which is asubset of the eight-allele combination mentioned above: HLA-C*07:01,HLA-DQA1*05:01, HLA-DQB1*02:01, HLA-DRB1*03:01, HLA-B*08:01, andHLA-DPB1*01:01. Three diseased samples (25%) had this combination, ascompared to 573 healthy samples (5.51%), which resulted in a FET p-valueof 2.55E-02 and OR 5.71 (95% CI 0.99-22.97).

After accounting for overlap of individuals with the distinct allelecombinations, we found that five diseased individuals (41.7%) had eitherof the last two combinations, while only 616 healthy samples (5.92%) hadat least one of the combinations. This resulted in FET 4.14E-04 and OR11.33 (95% CI 2.83-41.63).

Example 2. Further HLA Analysis of Patients with ADR Following Exposureto Infliximab

A set of 25 additional samples from subjects that had been treated withinfliximab and had experienced DILI were obtained. These are referred toas “cases” here. These samples were compared to a set of 60 matchedcontrols. The matched controls were patients who received infliximab forat least one year and did not experience DILI. The controls were matchedfor age, sex, ethnicity, and BMI where possible. Statistical analyseswere performed to identify from these cases HLA alleles that are riskfactors for the development of DILI following infliximab exposure.Significant alleles were determined using Fischer's Exact Test (FET)(p<0.05).

As a secondary comparison, the HLA profiles of the 25 cases werecompared to reference populations available atwww.allelefrequencies.net. For calculating population presence rates,reference list entries were found by searching for “Caucasoid” ethnicorigin subjects of gold-standard studies involving ≥100 subjects foralleles of interest on allelefrequencies.net. Sample sizes for thereferences represent the reported number of subjects directly typed fora given locus (i.e. USA NMDP European Caucasian reports 1,242,890subjects typed for HLA-B and DRB1, but only 395,676 subjects typed forHLA-C; see Table 5).

In order to test for significant differences between the 25Infliximab-DILI cases and the reference populations using Fisher's ExactTest (FET), counts of individuals carrying at least one copy of theallele in question were calculated one of two ways. If the populationpresence rate was available, the number of individuals was estimated byrounding the product of the population presence rate and the sample sizefor that HLA locus in that study. If no population presence rate wasavailable, this number was estimated using the allele frequency rate andassuming Hardy-Weinberg equilibrium (HWE). That is, if the allelefrequency is p, the number of individuals with the allele in questionwere calculated as [p²+2*p*(1−p)]*N_(samples), where p²+2*p*(1−p)represents the percentage of carriers if HWE is assumed, and N_(samples)is the reference sample size for that locus.

TABLE 5 Reference List Allele Ref # Sample Size Population ReferenceStudy B*39:01 Ref 1 1,242,890 USA NMDP European Caucasian Ref 2 298England Northwest C*12:03 Ref 1 395,676 USA NMDP European Caucasian Ref2 604 UK Pop 3 DRB1*03:01 Ref 1 1,242,890 USA NMDP European CaucasianRef 2 141 USA Philadelphia Caucasian DQB1*02:01 Ref 1 222 USA SanAntonio Caucasian Ref 2 141 USA Philadelphia Caucasian DQA1*3:03 Ref 1171 USA Caucasian Bethestda Ref 2 155 Netherlands pop 2

A summary of the alleles with significant results in the cases vs.controls individual data sets is provided in FIG. 5. The data setsindividually analyzed were: Caucasian typed and/or Caucasian imputed;African typed and/or African imputed; and All Ethnicities typed and/orAll Ethnicities imputed. “Typed only” means that only subjects withdirectly typed HLA alleles were considered in the indicated analysis.“Imputed only” means that only the imputed alleles (i.e., the subject'sHLA profile was determined using known proxies for HLA subtypes in theirgenetic sequence) for each subject were used in the indicated analysis.“Imputed+Typed” means that all subjects were considered; here, directlytyped HLA alleles were used if available, otherwise, imputed alleleswere used.

Table 6 provides a summary of the best reported FETs and associated OddsRatio (OR) for the indicated alleles. Of particular note, HLA-B*39:01was present in 4/25 cases and absent in 100% of controls, for an FET of6.25E-03 and an OR of 25.33.

TABLE 6 Summary of best reported FET Case Case Control Control VariantPresent Absent Present Absent FET OR Dataset HLA-B*39:01 4 21 0 606.25E−03 25.33 Caucasian imputed + typed HLA-C*12:03 6 19 3 57 1.69E−025.85 Caucasian imputed + typed HLA-DQA1*03:01 4 27 23 43 2.93E−02 0.28All ethnicities imputed + typed HLA-DPB1*04:02 3 0 1 5 4.76E−02 25.67African imputed + typed

Table 7A provides the overall presence rate and allele frequency of theindicated significant alleles in the cases and controls as compared tocalculated and/or estimated population presence rates (Ref 1 and/or Ref2). As above, significant alleles were determined using Fischer's ExactTest (FET) (p<0.05). The FET and associated Odds Ratio (OR) are reportedin Table 5B. In some cases the population presence rate—the percentageof individuals in the population who are expected to carry at least onecopy of the allele in question—is reported along with the allelefrequency rate as a whole, otherwise it is given as “NR” for “notreported” (Table 5A).

TABLE 7A Presence Rate and Allele Frequency Counts Cases ControlsPresence Rate (%) Allele Frequency Allele (25) (60) Cases Controls Ref 1Ref 2 Case Control Ref 1 Ref 2 B*39:01 4 0 16% 0.0% NR 1.3%  8% 0.0%1.1% 0.7% C*12:03 6 3 24% 5.0% NR 6.5% 12% 2.5% 4.9% 3.2% DRB1*03:01 108 40% 13.3% NR 15.6% 20% 6.7% 12.2% 7.8% DQB1*02:01 10 7 40% 11.7% NR15.6% 20% 5.8% 11.0% 7.8% DQA1*03:03 3 0 12% 0.0% 12.9% 13.5%  6% 0.0%7.3% 7.0%

TABLE 7B Fischer's Exact Test (FET) and Odds Ratio (OR) FET vs. OR vs.Allele Control Ref 1 Ref 2 Control Ref 1 Ref 2 B*39:01 0.01 0.00 0.0025.33 8.33 13.72 C*12:03 0.02 0.03 0.01 5.85 3.02 4.56 DRB1*03:01 0.010.05 0.01 4.24 2.25 3.57 DQB1*02:01 0.01 0.04 0.01 4.93 2.54 3.57DQA1*3:03 0.02 1.00 1.00 18.82 0.92 0.87

In summary, the studies showed that particular HLA alleles areassociated with a higher risk of DILI following infliximabadministration. In particular, HLA-B*39:01 was associated with a higherrisk of DILI. The studies also showed that a set of defined HLA alleles(and/or particular two-, three-, four-, five-, six-, seven-allele, ormore, combinations) are associated with higher risk of DILI followinginfliximab administration. The results of the study can be used toprovide new means of reducing the risk of DILI in patient populations,and/or new methods for treating autoimmune disease in the patientpopulations.

1. A method for treating an autoimmune disease in a subject in needthereof, comprising first determining that the subject has an HLAprofile that does not include an HLA-B*39:01 allele, wherein thenadministering infliximab to the subject.
 2. The method of claim 1,comprising: (i) obtaining a biological sample from the subject; (ii)detecting whether the HLA-B*39:01 allele is present in said biologicalsample; (iii) determining that the subject does not have the HLA-B*39:01allele, based on detecting the absence of said HLA alleles in step (ii);and then (iv) administering a therapeutically effective amount ofinfliximab to the subject.
 3. A method for treating an autoimmunedisease in a subject in need thereof, wherein the method comprisesdetermining that the subject does not have HLA-B*39:01 by obtaining orhaving obtained the HLA profile of the subject and then administeringinfliximab to the subject.
 4. The method of claim 1, wherein the HLAprofile is or has been obtained using a polymerase chain reaction(PCR)-based approach, a direct sequencing approach, a next generation(NGS) approach and/or a direct HLA typing test.
 5. The method of claim1, wherein the method comprises obtaining a biological sample from thesubject and performing a genetic assay to determine the absence ofallele HLA-B*39:01.
 6. The method of claim 5, further comprisingobtaining a PCR-amplified genomic DNA sample of the biological samplefrom the subject, contacting under hybridizing conditions the genomicDNA with an oligonucleotide that specifically hybridizes to HLA-B*39:01,and detecting the absence of HLA-B*39:01 in the sample.
 7. The method ofclaim 2, wherein the therapeutically effective amount is at least 5mg/kg infliximab.
 8. The method of claim 2, wherein the therapeuticallyeffective amount is about 5 mg/kg to about 10 mg/kg infliximab.
 9. Themethod of claim 2, wherein the therapeutically effective amount is about5 mg/kg infliximab.